def load(self):
"Rewrite load method"
PosCar.load(self)
with open(self.filename, 'r') as f:
for i in range(self.totline):
f.readline()
#get dimension of 3d array
grid = f.readline().strip(whitespace)
empty = not grid # empty row
while empty:
grid = f.readline().strip(whitespace)
empty = not grid
x, y, z = line2list(grid, dtype=int)
#read electron localization function data
elf_data = []
for line in f:
datalist = line2list(line)
elf_data.extend(datalist)
#########################################
# #
# !!! Notice !!! #
# NGX is the length of the **0th** axis #
# NGY is the length of the **1st** axis #
# NGZ is the length of the **2nd** axis #
# #
#########################################
#reshape to 3d array
elf_data = np.array(elf_data).reshape((x, y, z), order='F')
#set attrs
self.grid = x, y, z
self.elf_data = elf_data
return
def load(self):
"Rewrite load method"
PosCar.load(self)
with open(self.filename(), 'r') as f:
for i in xrange(self.totline):
f.readline()
#get dimension of 3d array
grid = f.readline().strip(whitespace)
empty = not grid # empty row
while empty:
grid = f.readline().strip(whitespace)
empty = not grid
x, y, z = line2list(grid, dtype=int)
#read electron localization function data
elf_data = []
for line in f:
datalist = line2list(line)
elf_data.extend(datalist)
#########################################
# #
# !!! Notice !!! #
# NGX is the length of the **0th** axis #
# NGY is the length of the **1st** axis #
# NGZ is the length of the **2nd** axis #
# #
#########################################
#reshape to 3d array
elf_data = np.array(elf_data).reshape((x, y, z), order='F')
#set attrs
self.grid = x, y, z
self.elf_data = elf_data
return
def load(self):
"Load all data in file into array."
data = []
with open(self.filename, 'r') as f:
for line in f:
line = line.strip()
if not line[0].isdigit(): # comment line or not
if not line.startswith('-'):
continue
elif not line[1].isdigit():
continue
linedata = line2list(line, field=self.field,
dtype=self.dtype)
data.append(linedata)
self.data = np.array(data)
return data
def load(self):
#locate informations
with open(self.filename(), 'r') as f:
total_forces = []
tforce_regex = \
re.compile(r'FORCES: max atom, RMS\s+(\d+\.\d+)\s+\d+\.\d+\s*')
max_regex = re.compile(r'Number: max atom\s+(\d+)\s*')
for i, line in enumerate(f):
#locate force infomation
if 'TOTAL-FORCE' in line: # force info begins
fbegin = i
elif 'RMS' in line: # total force
m = tforce_regex.search(line)
total_force = float(m.group(1))
total_forces.append(total_force)
elif 'Number' in line:
#atom number with max force on it
m = max_regex.search(line)
max_force_atom = int(m.group(1))
#get information details
#----------------- force info -------------------#
if 'fbegin' in dir():
#total force
total_forces = np.array(total_forces)
#atom forces
atom_forces = []
with open(self.filename(), 'r') as f:
for i, line in enumerate(f):
if i > fbegin+1:
if '-'*10 in line:
break
atom_force = line2list(line)
atom_forces.append(atom_force)
atom_forces = np.array(atom_forces)
#set attrs
self.total_forces = total_forces
self.atom_forces = atom_forces
self.max_force_atom = max_force_atom
else:
print ("Warning: " +
"the first electronic iteration is running, " +
"no force information is loaded.")
return
def load(self):
"Load all data in file into array."
data = []
with open(self.filename, 'r') as f:
for line in f:
line = line.strip()
if not line: # blank line
continue
if not line[0].isdigit(): # comment line or not
if not line.startswith('-'):
continue
elif not line[1].isdigit() and line[1] != '.':
continue
linedata = line2list(line, field=self.field, dtype=self.dtype)
data.append(linedata)
self.data = np.array(data)
return data
def load(self):
#locate informations
with open(self.filename(), 'r') as f:
total_forces = []
tforce_regex = \
re.compile(r'FORCES: max atom, RMS\s+(\d+\.\d+)\s+\d+\.\d+\s*')
max_regex = re.compile(r'Number: max atom\s+(\d+)\s*')
for i, line in enumerate(f):
#locate force infomation
if 'TOTAL-FORCE' in line: # force info begins
fbegin = i
elif 'RMS' in line: # total force
m = tforce_regex.search(line)
total_force = float(m.group(1))
total_forces.append(total_force)
elif 'Number' in line:
#atom number with max force on it
m = max_regex.search(line)
max_force_atom = int(m.group(1))
#get information details
#----------------- force info -------------------#
if 'fbegin' in dir():
#total force
total_forces = np.array(total_forces)
#atom forces
atom_forces = []
with open(self.filename(), 'r') as f:
for i, line in enumerate(f):
if i > fbegin + 1:
if '-' * 10 in line:
break
atom_force = line2list(line)
atom_forces.append(atom_force)
atom_forces = np.array(atom_forces)
#set attrs
self.total_forces = total_forces
self.atom_forces = atom_forces
self.max_force_atom = max_force_atom
else:
print("Warning: " + "the first electronic iteration is running, " +
"no force information is loaded.")
return
